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<<<<<<< Bend.cpp |
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#include "primitives/Bend.hpp" |
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namespace oopse { |
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|
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/**@todo still a lot left to improve*/ |
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void Bend::calcForce() { |
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|
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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Vector3d pos3 = atom3_->getPos(); |
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|
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Vector3d r12 = pos1 - pos2; |
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double d12 = r12.length(); |
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double d12inv = 1. 0 / d12; |
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|
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Vector3d r32 = pos3 - pos2; |
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double d32 = r32.length(); |
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double d32inv = 1. 0 / d32; |
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|
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double cosTheta = (r12*r32)/(d12*d32); |
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|
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//check roundoff |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
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} else if (cosTheta < -1.0) { |
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cosTheta = -1.0; |
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} |
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|
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double theta = acos(cosTheta); |
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|
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double firstDerivative; |
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bendType_->calcForce(theta, firstDerivative, potential_); |
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double sinTheta = sqrt(1.0 - cosTheta*cosTheta); |
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if(fabs(sinTheta) < 1.0E-12 ) { |
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sinTheta = 1.0E-12; |
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} |
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|
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double commonFactor1 = - firstDerivative / sinTheta * d12inv; |
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double commonFactor2 = - firstDerivative / sinTheta * d32inv; |
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|
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Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
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Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
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|
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//total force in current bend is zero |
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Vector3d force2 = force1 + force3; |
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force2 *= -1.0; |
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|
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atom1_->addFrc( force1); |
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atom2_->addFrc(force2); |
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atom3_->addFrc(force3); |
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|
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} |
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|
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double k = value->k * scale; |
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double theta0 = value->theta0; |
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|
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double diff = theta - theta0; |
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|
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double energy = k *diff*diff; |
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|
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double firstDerivative = 2.0 * k * diff; |
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|
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}//end namespace oopse |
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======= |
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#include "primitives/Bend.hpp" |
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|
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namespace oopse { |
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|
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/**@todo still a lot left to improve*/ |
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void Bend::calcForce() { |
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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Vector3d pos3 = atom3_->getPos(); |
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|
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Vector3d r12 = pos1 - pos2; |
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double d12 = r12.length(); |
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|
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double d12inv = 1.0 / d12; |
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|
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Vector3d r32 = pos3 - pos2; |
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double d32 = r32.length(); |
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|
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double d32inv = 1.0 / d32; |
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|
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double cosTheta = dot(r12, r32) / (d12 * d32); |
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|
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//check roundoff |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
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} else if (cosTheta < -1.0) { |
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cosTheta = -1.0; |
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} |
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|
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double theta = acos(cosTheta); |
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|
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double firstDerivative; |
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bendType_->calcForce(theta, firstDerivative, potential_); |
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|
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double sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
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if (fabs(sinTheta) < 1.0E-12) { |
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sinTheta = 1.0E-12; |
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} |
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double commonFactor1 = -firstDerivative / sinTheta * d12inv; |
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double commonFactor2 = -firstDerivative / sinTheta * d32inv; |
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Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
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Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
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|
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//total force in current bend is zero |
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Vector3d force2 = force1 + force3; |
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force2 *= -1.0; |
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|
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atom1_->addFrc(force1); |
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atom2_->addFrc(force2); |
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atom3_->addFrc(force3); |
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} |
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|
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} //end namespace oopse |
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>>>>>>> 1.2.2.4 |
